Two former Parramatta Eels players are accused of harbouring semi-automatic weapons and possessing more than half-a-million dollars in cash after dramatic arrests in Sydney's Centennial Park yesterday.

A former detective has told the reopened inquest into Daniel's 2003 death that Mr Condon told him to "f*** off" when he said he believed Cowan was the man responsible within weeks of the boy's disappearance.

Dennis Martyn said on Wednesday he concluded Cowan had abducted the 13-year-old soon after interviewing him.

He said he told Mr Condon, then the head of the Homicide Squad: "You've got Cowan, I think you'll find he's your man."

Daniel Morcombe's killer Brett Peter Cowan. (AAP)

But the former detective senior constable's theory was swiftly rejected.

Mr Condon said he made no apologies for not pursuing Cowan as a key suspect even though comfits resembled Cowan, who told police he drove past but didn't stop at the underpass where the abduction took place and that he did not see Daniel.

"I make no apologies for the decisions ... they were made in good faith," Mr Condon said.

Cowan is serving a life sentence for Daniel's murder. (AAP)

Cowan is serving a life sentence after being found guilty of Daniel's murder in 2014.

Mr Condon said there was not enough evidence to direct resources towards investigating Cowan and that there was really only a "gut feeling" about his involvement.

Mr Condon added more than 80 witnesses said they saw a blue car at the abduction site. Cowan owned a white vehicle.

"Up until 2011, I would never have approved his arrest," Mr Condon told the inquest.

The inquest also heard from Mr Martyn's former partner in the Major Incident Response (MIR) team Kenneth King, who said he had considered Cowan a key suspect.

Mr Condon said Mr King and Mr Martyn had verbally outlined their belief Cowan was a person of interest at an MIR team meeting at the time, but that was still not enough to pursue him.

"While it was interesting, no direct evidence implicated Cowan of any offence."

When asked by Peter Johns, counsel assisting, whether the fact that Cowan was in the vicinity at the time of the abduction wasn't enough to apply resources, Mr Condon replied: "You saying that's evidence?"

Chief Coroner Terry Ryan on Wednesday reopened the inquest into Daniel's abduction and murder more than five-and-a-half years after it was adjourned in 2011.

Both Mr Martyn and Mr King, who have since left the force, worked on the case for about two weeks as part of their duties with the MIR team before it was handed over to Homicide.

Mr King said he was concerned that his notebook was unavailable until Cowan's pre-trial hearing because it had been signed out for a fraud case, even though when he eventually checked it, there were no notes relating to fraud.

He also said audio files and photos attached to a report he filed during his MIR investigation were missing and the report had been truncated.

"Cowan was a very strong suspect. I thought it was odd, given the normal investigation practice," Mr King said. "No one had ever come back to me to clarify or check details."

He agreed with lawyer Peter Boyce, who is representing Daniel's parents Denise and Bruce Morcombe, that Cowan ticked a lot of boxes as a suspect.